SMTL ID : 7vrv.1

VAS5 Spike (1 RBD up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.20 Å

Oligo State

homo-trimer

Ligands

13 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: T.96, N.222, T.224 Chain C: K.450 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.698, N.906, Q.1052 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.906 NAG-NAG.3: 2 residues within 4Å: Chain A: K.776, N.782 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1079, T.1081, H.1082, F.1084 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1115 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: K.546 Chain B: N.268, N.270 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.782, Q.785 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1079, G.1080, H.1082, F.1084 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: I.1113, N.1115 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.698, F.699, L.903, Q.907 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.782, S.784, Q.785 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.1079, T.1081, H.1082 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: I.1113, V.1114, N.1115 No protein-ligand interaction detected (PLIP)

31 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.14: 2 residues within 4Å: Chain A: Y.16, N.49 Ligand excluded by PLIP NAG.15: 7 residues within 4Å: Chain A: V.108, N.110, N.113, V.115, F.145, Q.161, F.163 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.268, E.269, N.270 Chain C: K.546 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.319 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: G.327, F.330, N.331, S.359 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.591, T.592 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.604, R.634 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: H.643, N.645 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: S.689, N.690 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: E.1053, K.1054, N.1055 Chain B: Q.876 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: Y.16, N.18, F.47, N.49 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: T.96, N.222 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.319, Q.568 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.331, A.332, S.359 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.591, T.592 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.604, Q.632 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.645 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.690, N.691 Chain C: D.777 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.698, L.903, Q.907 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.1055 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain C: Y.16, T.17, N.18, F.47, S.48, N.49 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.222 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.270 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.319, Q.568 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.331, A.360, S.361 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.591, T.592 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.604, T.606 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: H.643, N.645 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.690 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: E.1053, N.1055 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.153 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhen, C. et al., VAS5 Spike(1 RBD up). To Be Published

Release Date

2022-06-22

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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